Eleven microsatellites were isolated from the vairone Leuciscus souffia (Risso 1826), an endangered fish that inhabits river systems in and around the Alps in Europe. The level of genetic diversity was assessed in 29 individuals of the subspecies L. s. souffia, and their variability was further estimated in seven individuals of a different subspecies, L. s. muticellus. Eight of these microsatellite loci were also applied to seven closely related cyprinid species. Availability of the reported microsatellite loci will facilitate the investigation of population genetic structure of these species with applications for the development of conservation strategies and phylogeographical approaches.